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Aliases for MIR4315-1 Gene

Subcategory (RNA class) for MIR4315-1 Gene

miRNA

Quality Score for this RNA gene is

3

Aliases for MIR4315-1 Gene

  • MicroRNA 4315-1 2 3
  • PLEKHM1 4 5
  • Pleckstrin Homology And RUN Domain Containing M1 5
  • PH Domain-Containing Family M Member 1 4
  • 162 KDa Adapter Protein 4
  • Hsa-Mir-4315-1 3
  • KIAA0356 4
  • AP162 4

External Ids for MIR4315-1 Gene

Previous GeneCards Identifiers for MIR4315-1 Gene

  • GC17U901476
  • GC17M043515
  • GC17Mp43514
  • GC17M043552
  • GC17M045475

Summaries for MIR4315-1 Gene

Entrez Gene Summary for MIR4315-1 Gene

  • microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

GeneCards Summary for MIR4315-1 Gene

MIR4315-1 (MicroRNA 4315-1) is an RNA Gene, and is affiliated with the miRNA class. Diseases associated with MIR4315-1 include Osteopetrosis, Autosomal Recessive 6. An important paralog of this gene is PLEKHM3.

UniProtKB/Swiss-Prot for MIR4315-1 Gene

  • Proposed to act as a multivalent adapter protein that regulates Rab7-dependent and HOPS complex-dependent fusion events in the endolysosomal system and couples autophagic and the endocytic trafficking pathways. Required for late stages of endolysosomal maturation, facilitating both endocytosis-mediated degradation of growth factor receptors and autophagosome clearance. Seems to be involved in the terminal maturation of autophagosomes and to mediate autophagosome-lysosome fusion (PubMed:25498145). Involved in vesicular transport in the osteoclast (By similarity). May be involved in negative regulation of endocytic transport from early endosome to late endosome/lysosome implicating its association with Rab7 (PubMed:20943950). May have a role in sialyl-lex-mediated transduction of apoptotic signals (PubMed:12820725). In case of infection contributes to Salmonella typhimurium pathogenesis by supporting the integrity of the Salmonella-containing vacuole (SCV) probably in concert with the HOPS complex and Rab7 (PubMed:25500191).

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for MIR4315-1 Gene

Genomics for MIR4315-1 Gene

Regulatory Elements for MIR4315-1 Gene

Enhancers for MIR4315-1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH17F045489 1 ENCODE 0.8 +0.1 53 1.8 HDGF ATF1 PKNOX1 ARID4B SIN3A GLI4 YBX1 ZNF48 ZNF121 ELK1 CRHR1-IT1 LRRC37A4P MIR4315-1 GC17M045480
GH17F045487 0.9 ENCODE 0.8 +2.6 2566 1.5 INSM2 KLF17 SIN3A ZNF2 ZEB1 ZNF366 SCRT2 FOS CEBPB TSHZ1 CRHR1-IT1 MAPK8IP1P1 MIR4315-1 GC17M045480
GH17F045483 0.6 Ensembl 0.4 +6.6 6649 2.2 ZNF664 GLIS2 IKZF1 ZMYM3 RAD21 CRHR1-IT1 LRRC37A GC17M045480 MIR4315-1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around MIR4315-1 on UCSC Golden Path with GeneCards custom track

Promoters for MIR4315-1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001347465 -151 1801 HDGF ATF1 PKNOX1 ARID4B SIN3A GLI4 YBX1 ZNF48 ZNF121 ELK1

Genomic Location for MIR4315-1 Gene

Chromosome:
17
Start:
45,435,900 bp from pter
End:
45,490,749 bp from pter
Size:
54,850 bases
Orientation:
Minus strand

Genomic View for MIR4315-1 Gene

Genes around MIR4315-1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
MIR4315-1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for MIR4315-1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for MIR4315-1 Gene

Proteins for MIR4315-1 Gene

  • Protein details for MIR4315-1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y4G2-PKHM1_HUMAN
    Recommended name:
    Pleckstrin homology domain-containing family M member 1
    Protein Accession:
    Q9Y4G2
    Secondary Accessions:
    • Q6P2R5
    • Q8TEL9
    • Q9NPP5
    • Q9NYA0

    Protein attributes for MIR4315-1 Gene

    Size:
    1056 amino acids
    Molecular mass:
    117443 Da
    Quaternary structure:
    • In colon carcinoma and breast carcinoma cells, it interacts with sialyl-lex-positive protein (PubMed:12820725). Interacts with RAB7A (GTP-bound form) (PubMed:20943950, PubMed:25500191). Interacts with VPS41, VPS11 and VPS39; indicative for an association with the HOPS complex; the interaction with VPS41 seems to require RAB7A (PubMed:25500191, PubMed:25498145). Interacts with GABARAP, GABARAPL, GABARAPL2, MAP1LC3A, MAP1LC3B and MAP1LC3C (PubMed:25498145). Interacts with PAFAH1B (By similarity). Interacts with Salmonella typhimurium sifA (PubMed:25500191).
    • In colon carcinoma and breast carcinoma cells, it interacts with sialyl-lex-positive protein (PubMed:12820725). Interacts with RAB7A (GTP-bound form) (PubMed:20943950, PubMed:25500191). Interacts with VPS41, VPS11 and VPS39; indicative for an association with the HOPS complex; the interaction with VPS41 seems to require RAB7A (PubMed:25500191, PubMed:25498145). Interacts with GABARAP, GABARAPL, GABARAPL2, MAP1LC3A, MAP1LC3B and MAP1LC3C (PubMed:25498145). Interacts with PAFAH1B (By similarity). Interacts with Salmonella typhimurium sifA (PubMed:25500191).
    Miscellaneous:
    • Sialyl-lex is a carcinoma associated antigen.
    SequenceCaution:
    • Sequence=BAA20813.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=CAB91652.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for MIR4315-1 Gene

neXtProt entry for MIR4315-1 Gene

Post-translational modifications for MIR4315-1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for MIR4315-1 Gene

Domains & Families for MIR4315-1 Gene

Gene Families for MIR4315-1 Gene

Protein Domains for MIR4315-1 Gene

Graphical View of Domain Structure for InterPro Entry

Q9Y4G2

UniProtKB/Swiss-Prot:

PKHM1_HUMAN :
  • The LIR (LC3-interacting region) motif mediates the interaction with ATG8 family proteins GABARAP, GABARAPL, GABARAPL2, and LC3A/B/C.
  • Contains 1 phorbol-ester/DAG-type zinc finger.
Domain:
  • The LIR (LC3-interacting region) motif mediates the interaction with ATG8 family proteins GABARAP, GABARAPL, GABARAPL2, and LC3A/B/C.
  • Contains 2 PH domains.
  • Contains 1 RUN domain.
Similarity:
  • Contains 1 phorbol-ester/DAG-type zinc finger.
genes like me logo Genes that share domains with MIR4315-1: view

No data available for Suggested Antigen Peptide Sequences for MIR4315-1 Gene

Function for MIR4315-1 Gene

Molecular function for MIR4315-1 Gene

UniProtKB/Swiss-Prot Function:
Proposed to act as a multivalent adapter protein that regulates Rab7-dependent and HOPS complex-dependent fusion events in the endolysosomal system and couples autophagic and the endocytic trafficking pathways. Required for late stages of endolysosomal maturation, facilitating both endocytosis-mediated degradation of growth factor receptors and autophagosome clearance. Seems to be involved in the terminal maturation of autophagosomes and to mediate autophagosome-lysosome fusion (PubMed:25498145). Involved in vesicular transport in the osteoclast (By similarity). May be involved in negative regulation of endocytic transport from early endosome to late endosome/lysosome implicating its association with Rab7 (PubMed:20943950). May have a role in sialyl-lex-mediated transduction of apoptotic signals (PubMed:12820725). In case of infection contributes to Salmonella typhimurium pathogenesis by supporting the integrity of the Salmonella-containing vacuole (SCV) probably in concert with the HOPS complex and Rab7 (PubMed:25500191).

Gene Ontology (GO) - Molecular Function for MIR4315-1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with MIR4315-1: view

Animal Model Products

miRNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for MIR4315-1 Gene

Localization for MIR4315-1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for MIR4315-1 Gene

Cytoplasm. Endosome membrane. Lysosome. Lysosome membrane. Note=Localizes to the external membrane of autolysosomes (PubMed:25498145). In case of infection colocalizes with Salmonella typhimurium sifA in proximity of Salmonella-containing vacuole (SCV) (PubMed:25500191). {ECO:0000269 PubMed:25498145, ECO:0000269 PubMed:25500191}.

Gene Ontology (GO) - Cellular Components for MIR4315-1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005764 lysosome IEA --
GO:0005765 lysosomal membrane IEA --
GO:0005768 endosome IEA --
GO:0010008 endosome membrane IEA --
genes like me logo Genes that share ontologies with MIR4315-1: view

No data available for Subcellular locations from COMPARTMENTS for MIR4315-1 Gene

Pathways & Interactions for MIR4315-1 Gene

SuperPathways for MIR4315-1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for MIR4315-1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006914 autophagy IEA --
GO:0015031 protein transport IEA --
GO:0035556 intracellular signal transduction IEA --
genes like me logo Genes that share ontologies with MIR4315-1: view

No data available for Pathways by source and SIGNOR curated interactions for MIR4315-1 Gene

Transcripts for MIR4315-1 Gene

mRNA/cDNA for MIR4315-1 Gene

(19) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Alternative Splicing Database (ASD) splice patterns (SP) for MIR4315-1 Gene

No ASD Table

Relevant External Links for MIR4315-1 Gene

GeneLoc Exon Structure for
MIR4315-1
ECgene alternative splicing isoforms for
MIR4315-1

Expression for MIR4315-1 Gene

mRNA Expression by UniProt/SwissProt for MIR4315-1 Gene:

Q9Y4G2-PKHM1_HUMAN
Tissue specificity: Expressed in placenta, liver, prostate, thymus, spleen, ovary, colon, colon carcinoma and peripheral blood lymphocytes (PBL). Weakly expressed in brain, lung, kidney, and testis. No expression in heart, skeletal muscle, pancreas and small intestine. Predominantly expressed in the breast carcinoma cell line MCF-7.

No data available for mRNA expression in normal human tissues , mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression and Protein tissue co-expression partners for MIR4315-1 Gene

Orthologs for MIR4315-1 Gene

This gene was present in the common ancestor of animals.

Orthologs for MIR4315-1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PLEKHM1 35
  • 99 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Plekhm1 35
  • 82 (a)
OneToOne
cow
(Bos Taurus)
Mammalia PLEKHM1 35
  • 79 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PLEKHM1 35
  • 79 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PLEKHM1 35
  • 71 (a)
OneToOne
chicken
(Gallus gallus)
Aves PLEKHM1 35
  • 61 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PLEKHM1 35
  • 56 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii plekhm1 35
  • 42 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea Y56A3A.16 35
  • 19 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea CSA.897 35
  • 37 (a)
OneToMany
Species where no ortholog for MIR4315-1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for MIR4315-1 Gene

ENSEMBL:
Gene Tree for MIR4315-1 (if available)
TreeFam:
Gene Tree for MIR4315-1 (if available)

Paralogs for MIR4315-1 Gene

Paralogs for MIR4315-1 Gene

Pseudogenes.org Pseudogenes for MIR4315-1 Gene

genes like me logo Genes that share paralogs with MIR4315-1: view

Variants for MIR4315-1 Gene

Sequence variations from dbSNP and Humsavar for MIR4315-1 Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type
rs11079565 -- 45,476,345(+) AAGAT(G/T)CAGGG intron-variant, upstream-variant-2KB
rs111658952 -- 45,475,609(+) TGCAG(A/C/T)AGCAG nc-transcript-variant, upstream-variant-2KB, reference, synonymous-codon, utr-variant-5-prime
rs112686965 -- 45,476,158(+) TTATA(C/T)ATAAT intron-variant, upstream-variant-2KB
rs112909686 -- 45,476,665(+) CAGAT(A/T)TTTGT intron-variant, upstream-variant-2KB
rs113308725 -- 45,476,166(+) AATAA(A/C)TATAT intron-variant, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for MIR4315-1 Gene

Variant ID Type Subtype PubMed ID
dgv123e55 CNV loss 17911159
dgv124e55 CNV loss 17911159
dgv1472n106 CNV deletion 24896259
dgv3274n100 CNV gain 25217958
dgv44n68 CNV loss 17160897
dgv45n68 CNV loss 17160897
esv2758691 CNV gain+loss 17122850
nsv1066765 CNV gain 25217958
nsv1070407 CNV deletion 25765185
nsv1120054 OTHER inversion 24896259
nsv1146669 OTHER inversion 26484159
nsv428342 CNV gain 18775914
nsv469875 CNV loss 16826518
nsv471504 CNV gain 19718026
nsv511056 OTHER complex 20534489

Relevant External Links for MIR4315-1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
MIR4315-1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for MIR4315-1 Gene

Disorders for MIR4315-1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for MIR4315-1 Gene - From: GeneCards

Disorder Aliases PubMed IDs
osteopetrosis, autosomal recessive 6
  • osteopetrosis autosomal recessive 6
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

PKHM1_HUMAN
  • Osteopetrosis, autosomal recessive 6 (OPTB6) [MIM:611497]: A rare genetic disease characterized by abnormally dense bone, due to defective resorption of immature bone. Osteopetrosis occurs in two forms: a severe autosomal recessive form occurring in utero, infancy, or childhood, and a benign autosomal dominant form occurring in adolescence or adulthood. Recessive osteopetrosis commonly manifests in early infancy with macrocephaly, feeding difficulties, evolving blindness and deafness, bone marrow failure, severe anemia, and hepatosplenomegaly. Deafness and blindness are generally thought to represent effects of pressure on nerves. {ECO:0000269 PubMed:17404618}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for MIR4315-1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
MIR4315-1
genes like me logo Genes that share disorders with MIR4315-1: view

No data available for Genatlas for MIR4315-1 Gene

Publications for MIR4315-1 Gene

  1. PLEKHM1 regulates autophagosome-lysosome fusion through HOPS complex and LC3/GABARAP proteins. (PMID: 25498145) McEwan D.G. … Dikic I. (Mol. Cell 2015) 4 64
  2. PLEKHM1 regulates Salmonella-containing vacuole biogenesis and infection. (PMID: 25500191) McEwan D.G. … Dikic I. (Cell Host Microbe 2015) 4 64
  3. Toward a comprehensive characterization of a human cancer cell phosphoproteome. (PMID: 23186163) Zhou H. … Mohammed S. (J. Proteome Res. 2013) 4 64
  4. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. (PMID: 20068231) Olsen J.V. … Mann M. (Sci. Signal. 2010) 4 64
  5. Rubicon and PLEKHM1 negatively regulate the endocytic/autophagic pathway via a novel Rab7-binding domain. (PMID: 20943950) Tabata K. … Yoshimori T. (Mol. Biol. Cell 2010) 4 64

Products for MIR4315-1 Gene

Sources for MIR4315-1 Gene

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